Bravo 16s and RNAseq Library Automation (Bravo Automations) 

16s ribosomal RNA sequencing can be used to identify and compare bacteria present within a given sample.

RNA-Seq is a powerful research tool for expression and variant analysis. Its’ application includes quantifying mRNA abundance; determining the transcriptional structure of genes: start sites, 5′ and 3′ ends, and splicing patterns; comparably detecting the changing expression levels of each transcript during development and under different conditions. It picks up all sequences that are present in the cell, regardless of their annotation status.

Gene Expression Core offers library preparation automation by Agilent Bravo Automation Workstation.The constructed libraries can be run on all NextGen sequencing platforms: Illumina HiSeq, MiSeq, and NextSeq.  Sequence can be done by ICBR NextGen Sequencing Core.

We also offer Agilent’s SureSelect Target Enrichment platform which allows you to focus your NextGen sequencing workflow on key genomic regions of interest while reducing cost per sample. Other NextGen relative services include cDNA library construction, normalization and rRNA depletion (Ribominus). If requested, we will directly deliver the libraries to our ICBR NextGen Sequencing Core with an e-mail notification to you.  Otherwise the library will be returned to you.

Custom Bravo Run (Bravo Automations) 

The service includes the Bravo consumables and run assistance.

For NEW customers and NEW projects: Schedule a consultation to discuss experimental design and prepare a project outline with an ICBR staff member.

This service allows the customer to do absolute quantification, rare allele detection, quantification using TaqMan SNP array and CNV (Copy Number Variation) in a more sensitive, specific, and precise way.

Agilent 2100 Bioanalyzer/2200 TapeStation Analysis (RNA DNA QC)

**Attention: If you are submitting libaries for a sequencing run in the NextGen core, please request their library evaluation services**

The Agilent 2100 Bioanalyzer and 2200 TapeStation system automatically perform the multiple steps of gel-based electrophoresis, replacing the need to run agarose gels to separate and quantitate your RNA or DNA samples.  A software tool, RNA Integrity Number (RIN) can help scientists estimate the integrity of total RNA samples.  Data is returned in the form of PDF.

Sample Concentration Measurement (RNA DNA QC)

Quantitate micro-volume of samples via NanoDrop, or Qubit. Please provide the DNA size if caculated nM concentration is needed.

RNA-Seq is a powerful research tool for expression and variant analysis. Its’ application includes quantifying mRNA abundance; determining the transcriptional structure of genes; start sits, 5′ and 3′ ends, and splicing patterns; comparably detecting the changing expression levels of each transcript during development and under different conditions. It picks up all sequences that are present in the cell, regardless of their annotation status.

The 10x Genomics Chromium Controller System

The 10X Genomics Chromium Controller instrument is designed to capture thousands of single cells or DNA fragment, and combined them with reagents and gel bead (which contains barcoded oligonucleotides) in emulsion droplets (GEMs) to perform a variety of assays. Each GEM are uniquely barcoded.

It can perform Single Cell RNA-seq, Single Cell Copy Number Variation Profiling, Single Cell Immune Repertoire Profiling, Single Nuclei Expression Profiling, and Single Cell CITE-seq. For those assays, it can capture 500-10,000 individual cells per sample. Additionally, it partitions high molecular weight (HMW) DNA into individual GEMs to capture long-range information using Illumina sequencer. This assay requires low input of high molecular weight DNA to produce “linked read” information, which can be used for assembling genomes, assessing structural variants and obtaining genome phase information.

General Service (qPCR)

qPCR analysis offered at Gene Expression and Genotyping are: SYBR® or TaqMan™ reagents allowing absolute, relative, relative standard or comparative Ct quantification. Services includes but not limited to qPCR Absolute Quantification Data Analysis/Per Standard Curve; RT Profiler PCR arrays – chemistry; qPCR post amplification read (SNP); qPCR Mid service  on CFX (1 plate); qPCR Plate set-up for 384 well Absolute Quantitation; qPCR primer and probe sets assay design.

 
Quantification of NextGen Sequencing libraries by qPCR 

This method is widely used because its ability to target adapter sequences for a specific sequences in NextGen libraries. It enables accurate quantification of NextGen libraries. It measures the functional molecular of the libraries.
 
SYBR Green-based Detection (qPCR)

This real-time PCR assay uses SYBR Green Chemistry to detect PCR products as it accumulate during real time PCR process.

 
TaqMan-based Detection (qPCR)

This real-time PCR assay consists a target-specific probe and two gene specific primes that can increase the specificity of quantification PCR. The fluorescence single generated by probe allows quantitate measurements of the accumulated PCR product and increases the specificity of gene detection.